Sixty-five AIDS patients with biopsy proven progressive multifocal leukoencephalopathy, PML, (the laboratory confirms the diagnosis using in situ DNA hybridization to detect viral DNA) were enrolled in a treatment study of ARA-C. Cerebrospinal fluid samples were taken at weekly intervals from 15 patients as treatment proceeded and assayed for viral JC Virus DNA. These patients were treated with ARA-C using intrathecal administration. PCR analysis of CSF samples revealed that 73% of the patients tested had JCV in their CSF at some time during the course of PML. In 4 cases, however, there was no evidence of viral DNA in their CSF during their treatment regime. These patients also did not have viral DNA in their blood. The study is now completed and the data are being evaluated. It does appear that the patients with either very low levels of viral DNA or no viral DNA in the CSF have a longer term survival compared with the other groups. This observation is critical to the prognosis of PML which until now has always been considered a uniformly fatal disease with little prospects for therapy. We have established a firm link between lymphoid and glial cells in the pathogenesis of JCV infection leading to demyelination in the human brain. We have screened over 60 tonsil tissues and found JCV DNA in 34% of these samples in either the stromal cell population and/or lymphocytes which traffic through the tonsil tissue. We have also identified the nucleotide sequences from the viral regulatory region in these tissues. The data indicate that the same viral genotype which is found in brain tissue of PML patients could originate from an initial lymphoid cell infection. This is the first evidence for a common route for JCV infection and establishes lymphoid cells as probable carriers of virus to other tissues. The molecular similarities between these cells for JCV gene expression and cells of the nervous system directly correlated with the expression of the NF- 1 class D family of DNA binding proteins which function for transcription. We have prepared polyclonal antibodies to each of the 4 classes of NF-1 and used these antibodies in gel shift experiments to identify class D proteins from both brain and lymphoid tissues. There appears to be a close association between susceptibility of infection to JCV and expression of this DNA binding protein.